MolNFT v1 · #96087 · protein + DNA
Human DNA polymerase eta-DNA ternary complex: misincorporation G opposite T after a C at the primer 3' end (CA/G)
4J9L: “Human DNA polymerase eta-DNA ternary complex: misincorporation G opposite T after a C at the primer 3' end…”. X-ray diffraction, 2 ligands (XG4, MG), 7 pockets (best druggability 0.81). MolNFT v1 #96087 on GenesisL1: 3D structure…
- PDB
- 4J9L
- Type
- protein + DNA
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; DNA
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- XG4, MG
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 430 | 45% helix, 22% strand | Q9Y253 |
| T | DNA | dna | 10 | — | — |
| P | DNA | dna | 9 | — | — |
Ligands and binding sites
- XG4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine · ligand · chains A, T, P
- MG · Magnesium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.81 | 0.83 | 70 | MG, XG4, GOL |
| 2 | 445 | 0.70 | 0.81 | 42 | empty |
| 3 | 209 | 0.65 | 0.84 | 25 | empty |
| 4 | 94 | 0.43 | 0.79 | 20 | empty |
| 5 | 89 | 0.36 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–T · 959 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–P · 658 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 370 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Compared structures
- 4J9L · Human DNA polymerase eta-DNA ternary complex: misincorporation G opposite T after a C at… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9Y253
- Elsewhere: RCSB PDB 4J9L · PDBe 4J9L · UniProt Q9Y253
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